rs2148575

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000658746.1(ENSG00000286543):​n.135+12953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 151,654 control chromosomes in the GnomAD database, including 54,605 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.82 ( 54605 hom., cov: 29)

Consequence

ENSG00000286543
ENST00000658746.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.245
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000286543ENST00000658746.1 linkn.135+12953A>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.821
AC:
124341
AN:
151536
Hom.:
54597
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.469
Gnomad AMI
AF:
0.906
Gnomad AMR
AF:
0.931
Gnomad ASJ
AF:
0.967
Gnomad EAS
AF:
0.887
Gnomad SAS
AF:
0.945
Gnomad FIN
AF:
0.902
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.972
Gnomad OTH
AF:
0.862
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.820
AC:
124381
AN:
151654
Hom.:
54605
Cov.:
29
AF XY:
0.822
AC XY:
60908
AN XY:
74088
show subpopulations
Gnomad4 AFR
AF:
0.469
Gnomad4 AMR
AF:
0.931
Gnomad4 ASJ
AF:
0.967
Gnomad4 EAS
AF:
0.887
Gnomad4 SAS
AF:
0.945
Gnomad4 FIN
AF:
0.902
Gnomad4 NFE
AF:
0.972
Gnomad4 OTH
AF:
0.863
Alfa
AF:
0.927
Hom.:
23424
Bravo
AF:
0.805
Asia WGS
AF:
0.902
AC:
3123
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
2.1
DANN
Benign
0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2148575; hg19: chr5-34258465; API